puzzle picture
1445: Aflatoxin Challenge: Round 2 with Insertions
Status: Closed

Summary

Name: 1445: Aflatoxin Challenge: Round 2 with Insertions
Status: Closed
Created: 10/31/2017
Points: 100
Expired: 11/14/2017 - 23:00
Difficulty: Intermediate
Description: Aflatoxins are a class of poisonous compounds that contaminate a significant portion of the global food supply. In this puzzle, players are challenged to redesign an enzyme that could break down aflatoxin molecules. The majority of the protein is frozen, with the aflatoxin ligand fixed in a binding pocket. Surrounding the binding pocket are a number of loops that might be redesigned without affecting the folding stability of the protein. In these loops, players may manipulate the protein backbone and mutate the residue sidechains. Players may add up to 20 additional residues within these loops, at a cost of 16 points per residue. Players may load in solutions from Puzzle 1440.

This is the second puzzle of our Aflatoxin Challenge, sponsored by Mars Inc. and Thermo Fisher Scientific. Promising designs will be tested by the Siegel Lab at UC Davis. By participating in the challenge/game, the players agree that all player designs will be available permanently in the public domain, and the players will not seek intellectual property protection over the designs created as part of the challenge/game.
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 1 hour 23 min ago. Offline
Joined: 11/15/2012
Groups: None
Puzzle expires November 14

Apologies, the puzzle was originally posted with an incorrect expiration date. This puzzle will expire on November 14 at 23:00 UTC.

Joined: 09/24/2012
Groups: Go Science
Should be out of global ranking

Due to ambiguous private companies sponsoring (for this puzzle series only), I suggest this puzzle series being set outside of global and Overall rankings (if not in a separate category called "sponsored") in order not to penalize the players who wouldn't want to participate.

Personally, I'd feel more comfortable to freely participate in any project "outside" the normal Foldit conditions, exactly as I would participate in Contests and any other "devprev" non (global ranking) rewarding puzzles.

Joined: 05/19/2017
Groups: None
Could you explain further?

As I'm unfamiliar to the scene I'm having trouble understanding why contest or event puzzles shouldn't give players global points for their rank. Why does sponsorship dissuade players from participating? Shouldn't it have the opposite effect where it gives players a better chance for their solution to be tested and credited?

Joined: 09/24/2012
Groups: Go Science
here some explanation

http://fold.it/portal/node/2004322#comment-35645

Concerning contests not being rewarded, it's linked to the fact that researchers want to reward what is potentially useful for their scientific project. We are more in a Citizen Science context than pure gaming context.

Joined: 05/19/2017
Groups: None
That clarifies things

It's those extended causality outside factors that ties the hands, I see. More and more gaming media outlets and individuals are adding ad or sponsored tags to their content, which is the most relevant example I can relate to this. Kinda muddles the value of global score if it was counted for global score huh?

This is something that I think would need to be addressed in an overhaul of Foldit's progression and leaderboard system, though it's not something I have a nuanced solution for from the top of my head.

LociOiling's picture
User offline. Last seen 1 hour 11 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
bonding sites for aflatoxin

The aflatoxin ligand in this puzzle is the same as in puzzle 1440. The puzzle starts with three bonds between locked sections of the protein and the aflatoxin.

The atom numbers for the ligand were identified in a previous post.

Here's another view of the ligand, showing the starting bonds and the bondable atoms of the ligand. The view settings are "show bonds (sidechain)", "show bonds (non-protein)", "show bondable atoms", "EnzDes" color, "Cartoon Ligand" view, and "show all" sidechains.

In the ligand, all of the possible hydrogen bond donors and acceptors are oxygen atoms.

The type of hydrogen bond each oxygen can accept depends on how the atom is already bound.

Aflatoxin bondable atoms: Hydrogen bond donors and acceptors for the ligand in puzzles 1440 and 1445, along with starting bonds.Aflatoxin bondable atoms: Hydrogen bond donors and acceptors for the ligand in puzzles 1440 and 1445, along with starting bonds.



Ligand atoms 2 and 6 can act as hydrogen bond acceptors. Ligand atoms 12, 16, 22, 23, and 25 can act as either hydrogen bond acceptors or hydrogen bond donors.

The starting bonds are:

segment amino acid atom ligand
atom
length
131 asparagine 8 23 2.92
188 asparagine 8 25 3.18
239 aspartate 7 25 2.56

The bonds were determined by drawing bands with a script.

alcor29's picture
User offline. Last seen 22 hours 34 min ago. Offline
Joined: 11/16/2012
Aflatoxin 1445

The reverse (grayed/frozen) side of the aflatoxin grabber seems to have the structure of an ideal funnel trap to let the aflatoxin enter or even be 'sucked' in. If that's true and the funnel side-chains don't clog the passage, what we need to do is to block the rear entrance and 'grab' the aflatoxin in the 'pocket' like a baseball in a glove to keep if from getting through or backing out. What do you think?

Susume's picture
User is online Online
Joined: 10/02/2011
More info in science chat log

There was some great discussion from the scientists about whether it's important to leave an opening for the aflatoxin to get in/out of the protein (turns out, not very important), and whether it's important that all the bondable atoms either have bonds on them or are exposed on the surface (turns out, very important): http://fold.it/portal/node/2004407

Joined: 09/24/2012
Groups: Go Science
What is the contribution of the sponsors?

Why this sentence which seems a repetition of normal Foldit Conditions?

"By participating in the challenge/game, the players agree that all player designs will be available permanently in the public domain, and the players will not seek intellectual property protection over the designs created as part of the challenge/game"

bkoep's picture
User offline. Last seen 1 hour 23 min ago. Offline
Joined: 11/15/2012
Groups: None
Sponsors funding labwork

The sponsors are funding the experiments that will test Foldit designs in the lab (lab research is expensive!). Without the contributions from Mars Inc. and Thermofisher Scientific, we would not be able to test Foldit player designs to see if they actually bind and degrade aflatoxin.

The last sentence of the puzzle description is NOT a repetition of the Foldit Terms of Service. In fact, it is quite different from our normal ToS, which is why the statement is included in all Aflatoxin Challenge puzzle descriptions.

Our regular ToS affirms that scientific discoveries from regular puzzles can indeed be patent protected, and that relevant players will be considered co-inventors on any patent applications. At the request of our sponsors, Aflatoxin Challenge puzzles are different from regular puzzles; all aflatoxin player designs will remain in the public domain, and are not eligible for patent protection.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons